Hi Chris,
I'm a Dob user with digital setting circles, but think I have a basic idea how to use manual setting circles on an Equatorial mount. Here goes...
1. You need to remember that RA is a static measure for the position of an astronomical object (ie. from Greenwich london, at the point in the year when the March Equinox occurs). The is a good description on Wikipedia.
http://en.wikipedia.org/wiki/Right_ascension
2. Sounds like you've done al the tricky stuff already. Only think you need to do is twirl your RA circle to match the "Star Atlas" RA when you line up on a known object. As an example, point at Sirius then adjust your RA circle to read 6 hrs, 45 min.
3. Of course, you may need to re-adjust on Sirius a few times through the night if you want to locate some more distant fuzzies using RA/DEC coordinates
Hope this helps.